pdom.Simulate¶

class pdom.Simulate(config_file, out_folder=None, data_file=None, overwrites=None, resolution=250)¶

Class to simulation different degradation models

Parameters:	config_file (str, Path) – .ini file to load out_folder (str, Path, optional) – folder to save the results data_file (str, Path, optional) – .json file containing experimental data overwrites (dict, optional) – overwrite settings from the config file resolution (int, optional) – time resolution for data export

cfg = None¶: the simulation configuration created with pdom.data.Parameter from the config file.

rhs_bonds(t, N_flat, k, N_shape)¶

Right-hand site for multi species model excess_bonds.

Calculate the derivative for a given concentration profile.

Parameters:	N_flat (ndarray) – number of molecules \| 3-dim flattened t (float) – time (not used) k (ndarray) – simulation constants (\(k_{\mathrm{ads}}\), \(k_{\mathrm{des}}\), \(k_{\mathrm{reac}}\)) N_shape (tuple) – original shape of N

first dimension of N corresponds to the number of Carbon atoms carbon_count=index+1
second dimension of N corresponds to the number of excess bonds excess_bonds=index
max(excess_bonds) < max(carbon_count)
N[:, :, 0] is the number of molecules on the surface
N[:, :, 1] is the number of molecules in solution
the simulation constants must have the shape (3, max(excess_bonds)+1, max(carbon_count))

Returns:	first derivative
Return type:	ndarray

rhs_multi(t, N_flat, k, N_shape)¶

Right-hand site for multi species models fragmentation and incremental.

Calculate the derivative for a given concentration profile.

Parameters:	N_flat (ndarray) – number of molecules \| 2-dim flattened t (float) – time (not used) k (ndarray) – simulation constants (\(k_{\mathrm{ads}}\), \(k_{\mathrm{des}}\), \(k_{\mathrm{reac}}\)) N_shape (tuple) – original shape of N

first dimension of N corresponds to the number of Carbon atoms carbon_count=index+1
N[:, 0] is the number of molecules on the surface
N[:, 1] is the number of molecules in solution
the simulation constants must have the shape (3, max(carbon_count))

Returns:	first derivative
Return type:	ndarray

rhs_single(t, N, k)¶

Right-hand site for single species model.

Calculate the derivative for a given concentration profile.

Parameters:	N (ndarray) – number of molecules \| 1-dim t (float) – time (not used) k (ndarray) – simulation constants (\(k_{\mathrm{ads}}\), \(k_{\mathrm{des}}\), \(k_{\mathrm{reac}}\))

Returns:	first derivative
Return type:	ndarray

run()¶: Runs either a simulation or performs a parameter fit based on the information stored in cfg. The results are saved to the file system.